In this section

Arabidopsis thaliana vs Prunus persica LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterArabidopsis thalianaPrunus persica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 127,079 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 83,147,367 out of 119,667,750
Covered: 36,520,383 out of 119,667,750

Uncovered: 7,873,151 out of 33,775,569
Matches: 17,697,132 out of 33,775,569
Mismatches: 7,671,864 out of 33,775,569
Insertions: 533,422 out of 33,775,569
Identity over aligned base-pairs: 68.3%

Prunus persica

Uncovered: 188,954,612 out of 227,411,381
Covered: 38,456,769 out of 227,411,381

Uncovered: 8,548,783 out of 33,236,255
Matches: 16,577,933 out of 33,236,255
Mismatches: 7,395,024 out of 33,236,255
Insertions: 714,515 out of 33,236,255
Identity over aligned base-pairs: 67.2%

Block size distribution

Size range All 127,079 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,232
7.1 kb
10 bp - 100 bp
18,804
1.2 Mb
3,728
262.9 kb
100 bp - 1 kb
95,790
34.1 Mb
21,326
8.2 Mb
1 kb - 10 kb
11,252
17.0 Mb
13,344
32.3 Mb
10 kb - 100 kb
1
10.6 kb
489
10.1 Mb
100 kb - 1 Mb
9
1.4 Mb